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Explicit equilibrium modeling of transcription-factor binding and gene regulation.

Publication ,  Journal Article
Granek, JA; Clarke, ND
Published in: Genome Biol
2005

We have developed a computational model that predicts the probability of transcription factor binding to any site in the genome. GOMER (generalizable occupancy model of expression regulation) calculates binding probabilities on the basis of position weight matrices, and incorporates the effects of cooperativity and competition by explicit calculation of coupled binding equilibria. GOMER can be used to test hypotheses regarding gene regulation that build upon this physically principled prediction of protein-DNA binding.

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Published In

Genome Biol

DOI

EISSN

1474-760X

Publication Date

2005

Volume

6

Issue

10

Start / End Page

R87

Location

England

Related Subject Headings

  • Transcription Factors
  • Saccharomyces cerevisiae Proteins
  • Repressor Proteins
  • Protein Binding
  • Promoter Regions, Genetic
  • Oligonucleotide Array Sequence Analysis
  • Nuclear Proteins
  • Models, Genetic
  • Genes, cdc
  • Gene Expression Regulation
 

Citation

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ICMJE
MLA
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Granek, J. A., & Clarke, N. D. (2005). Explicit equilibrium modeling of transcription-factor binding and gene regulation. Genome Biol, 6(10), R87. https://doi.org/10.1186/gb-2005-6-10-r87
Granek, Joshua A., and Neil D. Clarke. “Explicit equilibrium modeling of transcription-factor binding and gene regulation.Genome Biol 6, no. 10 (2005): R87. https://doi.org/10.1186/gb-2005-6-10-r87.
Granek, Joshua A., and Neil D. Clarke. “Explicit equilibrium modeling of transcription-factor binding and gene regulation.Genome Biol, vol. 6, no. 10, 2005, p. R87. Pubmed, doi:10.1186/gb-2005-6-10-r87.

Published In

Genome Biol

DOI

EISSN

1474-760X

Publication Date

2005

Volume

6

Issue

10

Start / End Page

R87

Location

England

Related Subject Headings

  • Transcription Factors
  • Saccharomyces cerevisiae Proteins
  • Repressor Proteins
  • Protein Binding
  • Promoter Regions, Genetic
  • Oligonucleotide Array Sequence Analysis
  • Nuclear Proteins
  • Models, Genetic
  • Genes, cdc
  • Gene Expression Regulation